The city of Fair Haven is set within 19th-century Ireland. While driving along a road, Tom Paris crashes his vintage automobile. Seamus Driscol, one of the townsfolk, cannot believe his eyes when he sees Paris' tire magically repair itself. He immediately heads to Sullivan's Pub, and tells its inhabitants that he believes Tom is from the spirit world.

Back in town, Kim and Maggie are walking together and holding hands. Meanwhile, they are unaware that Seamus and Milo are watching their every move. Just as the two are about to kiss, Paris plays a trick on Kim by morphing Maggie into a cow in a holographic effect. Kim can hear Paris laughing, just as they are instructed through a com call to return to the bridge.

Seamus tells his priest exactly what he saw. Acting as his priest, the Doctor tells Seamus that Tom Paris is a known prankster and that he is not to worry. Later that day, Seamus and Milo run into Maggie who tells them that she feels like she woke up from the strangest dream where she was walking around town with a bell around her neck.

Soon, the townsfolk gather and exchange similar stories. Michael Sullivan tells Katie that the townsfolk think that she and her friends are not from this earth. Because he believes that Katie is lying to him, Janeway decides to end the program. Back on Voyager, Janeway doesn't know how the holodeck characters could possibly be asking so many questions about their origin.

Back on Voyager, Paris instructs the computer to display all of Fair Haven's characters. Michael Sullivan appears and is suprisingly aware of his surroundings. Kim discovers that each characters' perceptual filters are off-line. The Voyager crew decides that they will repair the malfunction by accessing each of the characters' controls from Sullivan's Pub.

Back at Sullivan's Pub, Michael remembers being "spirited" away to an unknown place where there was talk of changing the people of Fair Haven. At the church, several of the townfolk begin to assemble and warrant their concerns. They storm into Sullivan's Pub, where Kim and Paris are working on the Starfleet control panel. Before the two can react, a net of red twine is thrown over them, knocking them to the ground. Milo suddenly fires his gun at the panel which causes sparks to fly. Paris instructs the computer to freeze the program, but since it is damaged only some of the animated townsfolk are frozen.

Paris and Kim are soon on the run with the mob of townsfolk following close behind. They instruct the computer to exit the program, but unfortunately their commands are unrecognized. Meanwhile on Voyager, Torres suggests cutting power to the hologrid. Although the inhabitants of Fair Haven are not real people, but rather holograms, Janeway possesses genuine feelings towards them.

Paris and Kim find themselves tied to chairs near the altar of the church. Reading from a thick, old book, Seamus demands the return of the prisoners to the otherworld. Nothing happens and Seamus instructs the others to tie the Doctor up as well.

Seamus hypnotizes the Doctor, asking him questions about banishing the spirit-folk to the "otherworld." The Doctor begins to tell them about Voyager, and Michael demands that he instruct him on how to be transported to Katie's location.

Janeway tries to explain to Michael that they are simply explorers that like to spend time in Fair Haven. Janeway and Michael both return to the holodeck, and Michael tries to calm the townsfolk down, insisting that the Voyager crew means no harm.

While the damaged holodeck is being repaired, the Voyager crew decides to have one last night at Sullivan's Pub before Fair Haven is temporarily put to rest. It is clear that Janeway and Michael have formed a special bond with one another, as Michael reaches and takes her hand.